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A robust KASP marker for selection of four pairs of linked leaf rust and stripe rust resistance genes introgressed on chromosome arm 5DS from different wheat genomes

Molecular Biology Reports volume 48, pages 5209–5216 (2021)Cite this article

Abstract

Stripe rust and leaf rust are among the most devastating diseases of wheat, limiting its production globally. Wheat wild relatives harbour genetic diversity for new genes and alleles for all major wheat diseases. However, the use of this genetic variation from wild progenitor and non-progenitor species has been limited in the breeding programs. Reasons include limited recombination of donor and recipient genomes and the lack of tertiary gene pool markers. Here, we describe the development of a SNP based marker from the flow-sorted and sequenced Aegilops umbellulata chromosome 5U which can be used for marker assisted selection of four pair of alien leaf rust and stripe rust resistance genes. Lr57-Yr40_CAPS16 marker was reported earlier to be linked with alien leaf and stripe rust resistance genes introgressed on wheat chromosome 5DS. Due to its dominant nature and laborious to work with, a new SNP-based KASP marker, XTa5DS-2754099_kasp23, was developed from the same CAPS marker contig. XTa5DS-2754099_kasp23 was tested in Aegilops umbellulata, Ae. geniculata, Ae. peregrina and Ae. caudata derived alien introgression lines, which harbour four pairs of linked leaf and stripe rust genes; Lr76-Yr70, Lr57-Yr40, LrP- YrP, LrAc-YrAc, respectively. This KASP marker was found to be effective for the selection of the aforesaid four pairs of leaf rust and stripe rust resistance genes. Further, we tested and validated XTa5DS-2754099_kasp23 on commercial varieties and advanced breeding lines from four countries (India, Egypt, Australia and UK) including hexaploid and durum wheat. Our results provide evidence that KASP marker, XTa5DS-2754099_kasp23 can be used in marker-assisted selection of the four pairs of rust resistance alien genes in wheat breeding programmes.

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Data availability

All the data generated or analysed during this study are included in the published article and its supplementary information file. The material is available from the corresponding author on reasonable request.

References

  1. Engering A, Hogerwerf L, Slingenbergh J (2013) Pathogen–host–environment interplay and disease emergence. Emerg Microbes Infect 2(2):e5

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Mastretta-Yanes A, Gasman FA, Burgeff C, Ramírez MC, Piñero D, Sarukhán J (2018) An initiative for the study and use of genetic diversity of domesticated plants and their wild relatives. Front Plant Sci 9:209

    Article  Google Scholar 

  3. Zhang H, Mittal N, Leamy LJ, Barazani O, Song BH (2016) Back into the wild-apply untapped genetic diversity of wild relatives for crop improvement. Evol Appl 10(1):5–24

    Article  Google Scholar 

  4. Borrill P, Harrington SA, Uauy C (2019) Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat. Plant J 97(1):56–72

    CAS  PubMed  Google Scholar 

  5. Brozynska M, Furtado A, Henry R (2015) Genomics of crop wild relatives: expanding the gene pool for crop improvement. Plant Biotechnol J 14:1070–1085

    Article  Google Scholar 

  6. Li H, Deal KR, Luo M-C, Ji W, Distelfeld A, Dvorak J (2017) Introgression of the Aegilops speltoides Su1-Ph1 suppressor into wheat. Front Plant Sci 8:2163

    Article  Google Scholar 

  7. Martin AC, Rey MD, Shaw P, Moore G (2017) Dual effect of the wheat Ph1 locus on chromosome synapsis and crossover. Chromosoma 126:669–680

    Article  CAS  Google Scholar 

  8. Rey MD, Calderón MC, Prieto P (2015) The use of the ph1b mutant to induce recombination between the chromosomes of wheat and barley. Front Plant Sci 6:160

    Article  Google Scholar 

  9. Edet OU, Kim J, Okamoto M, Hanada K, Takeda T, Kishii M, Gorafi YSA, Tsujimoto S (2018) Efficient anchoring of alien chromosome segments introgressed into bread wheat by new Leymus racemosus genome-based markers. BMC Genet 19:18

    Article  CAS  Google Scholar 

  10. Thomson MJ (2014) High-throughput SNP genotyping to accelerate crop improvement. Plant Breed Biotechnol 2:195–212

    Article  Google Scholar 

  11. Hussain W, Baenziger PS, Belamkar V, Guttieri MJ, Venegas JP, Easterly A, Sallam A, Poland J (2017) Genotyping-by-sequencing derived high-density linkage map and its application to QTL mapping of flag leaf traits in bread wheat. Sci Rep 7:16394

    Article  Google Scholar 

  12. Poland JA, Brown PJ, Sorrells ME, Jannink JE (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by- sequencing approach. PLoS ONE 7:e32253

    Article  CAS  Google Scholar 

  13. Wang S, Wong D, Forrest K, Allen A, Chao S, Huang BE et al (2014) Characterization of polyploid wheat genomic diversity using a high-density 90000 single nucleotide polymorphism array. Plant Biotechnol J 12:787–796

    Article  CAS  Google Scholar 

  14. Semagn K, Babu R, Hearne S, Olsen M (2013) Single nucleotide polymorphism genotyping using kompetitive allele specific PCR (KASP): overview of the technology and its application in crop improvement. Mol Breed 33:1–14

    Article  Google Scholar 

  15. Tiwari VK, Wang S, Sehgal S, Vrána J, Friebe B, Kubaláková M, Chhuneja P, Doležel J, Akhunov E, Kalia B, Sabir J, Gill BS (2014) SNP discovery for mapping alien introgressions in wheat. BMC Genom 15:273–284

    Article  Google Scholar 

  16. Kumari N, Gina BG, Li H (2013) Development and validation of a breeder-friendly KASPar marker for wheat leaf rust resistance locus Lr21. Mol Breed 31:233–237

    Article  Google Scholar 

  17. Forrest K, Pujol V, Bulli P, Pumphrey M, Wellings C, Herrera-Foessel S, Huerta-Espino J, Singh R, Lagudah E, Hayden M, Spielmeyer W (2014) Development of a SNP marker assay for the Lr67 gene of wheat using a genotyping by sequencing approach. Mol Breed 34:2109–2118

    Article  CAS  Google Scholar 

  18. Klymiuk V, Yaniv E, Huang L, Raats D, Fatiukha A, Chen S, Feng L, Frenkel Z, Krugman T, Lidzbarsky G, Chang W, Jääskeläinen MJ, Schudoma C, Paulin L, Laine P, Bariana H, Sela H, Saleem K, Sørensen CK, Hovmøller MS, Distelfeld A, Chalhoub B, Dubcovsky J, Korol AB, Schulman AH, Fahima T (2018) Cloning of the wheat Yr15 resistance gene sheds light on the plant tandem kinase-pseudokinase family. Nat Commun 9:3735

    Article  Google Scholar 

  19. Marchal C, Zhang J, Zhang P, Fenwick P, Steuernagel B, Adamski N, Boyd L, Mcintosh R, Wulff B, Berry S, Lagudah E, Uauy C (2018) BED-domain containing immune receptors confer diverse resistance spectra to yellow rust. Nat Plants 4:662–668

    Article  CAS  Google Scholar 

  20. Narang D, Kaur S, Steuernagel B, Ghosh S, Dhillon R, Bansal M, Uauy C, Wulff BBH, Chhuneja P (2019) Fine mapping of Aegilops peregrina co-segregating leaf and stripe rust resistance genes to distal most end of 5DS. Theor Appl Genet. https://doi.org/10.1007/s00122-019-03293-5

    Article  PubMed  Google Scholar 

  21. Grewal S, Hubbart-Edwards S, Yang C, Devi U, Baker L, Heath J, Ashling S, Scholefield D, Howells C, Yarde J, Isaac P, King IP, King J (2020) Rapid identification of homozygosity and site of wild relative introgressions in wheat through chromosome-specific KASP genotyping assays. Plant Biotechnol J 18:743–755

    Article  CAS  Google Scholar 

  22. Wright SI, Bi IV, Schroeder SC et al (2005) Evolution: the effects of artificial selection on the maize genome. Science 308:1310–1314

    Article  CAS  Google Scholar 

  23. Mardis ER (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24:133–141

    Article  CAS  Google Scholar 

  24. Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS (2007) SNP discovery via 454 transcriptome sequencing. Plant J 51:910–918

    Article  CAS  Google Scholar 

  25. Trick M, Long Y, Meng J, Bancroft I (2009) Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. Plant Biotechnol J 7:334–346

    Article  CAS  Google Scholar 

  26. Novaes E, Drost DR, Farmerie WG et al (2008) Highthroughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genom 9:312

    Article  Google Scholar 

  27. Bundock PC, Eliott FG, Ablett G et al (2009) Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing. Plant Biotechnol J 7:347–354

    Article  CAS  Google Scholar 

  28. Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA (2010) Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genom 11:180

    Article  Google Scholar 

  29. Lai K, Duran C, Berkman PJ et al (2012) Single nucleotide polymorphism discovery from wheat next-generation sequence data. Plant Biotechnol J 10:743–749

    Article  CAS  Google Scholar 

  30. Molnar I, Kubalakova M, Simkova H, Cseh A, Molnar-Lang M, Dolezel J (2011) Chromosome isolation by flow sorting in Aegilops umbellulata and Ae. comosa and their Allotetraploid hybrids Ae biuncialis and Ae geniculata. PLoS ONE 6:27708

    Article  Google Scholar 

  31. Bansal M, Adamski N, Toor P, Kaur S, Istvan M, Holušová K, Vrána J, Dolezel J, Valárik M, Uauy C, Chhuneja P (2020) Aegilops umbellulata introgression carrying leaf rust and stripe rust resistance genes Lr76 and Yr70 located to 9.47-Mb region on 5DS telomeric end through a combination of chromosome sorting and sequencing. Theor App Genet 133:903–915. https://doi.org/10.1007/s00122-019-03514-x

    Article  CAS  Google Scholar 

  32. Bansal M, Kaur S, Dhaliwal HS, Bains NS, Bariana HS, Chhuneja P, Bansal UK (2017) Mapping of Aegilops umbellulata-derived leaf rust and stripe rust resistance loci in wheat. Plant Pathol 66:38–44

    Article  CAS  Google Scholar 

  33. Kuraparthy V, Sood S, See DR, Gill BS (2009) Development of a PCR assay and marker-assisted transfer of leaf rust and stripe rust resistance genes Lr57 and Yr40 into hard red winter wheats. Crop Sci 49:120–126

    Article  CAS  Google Scholar 

  34. Toor PI, Kaur S, Bansal M, Yadav B, Chhuneja P (2016) Mapping of stripe rust resistance gene in an Aegilops caudata introgression line in wheat and its genetic association with leaf rust resistance. J Genet 95:933–938

    Article  CAS  Google Scholar 

  35. Kuraparthy V, Chhuneja P, Dhaliwal HS, Kaur S, Bowden RL, Gill BS (2007) Characterization and mapping of cryptic alien introgression from Aegilops geniculata with novel leaf rust and stripe rust resistance genes Lr57 and Yr40 in wheat. Theor Appl Genet 114:1379–1389

    Article  CAS  Google Scholar 

  36. International Wheat Genome Sequencing Consortium (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345:1251788

    Article  Google Scholar 

  37. Riar AK, Kaur S, Dhaliwal HS, Singh K, Chhuneja P (2012) Introgression of a leaf rust resistance gene from Aegilops caudata to bread wheat. J Genet 91:155–161

    Article  CAS  Google Scholar 

  38. Lorieux M (2012) MapDisto: fast and efficient computation of genetic linkage maps. Mol Breed 30:1231–1235

    Article  CAS  Google Scholar 

  39. Voorrips RE (2002) Map chart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78

    Article  CAS  Google Scholar 

  40. Peterson RF, Campbell AB, Hannah AE (1948) A diagnostic scale for estimating rust severity on leaves and stem of cereals. Can J Res 26:490–500

    Google Scholar 

  41. International Wheat Genome Sequencing Consortium, Appels R, Eversole K, Stein N, Feuillet C et al (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361:eaar7191. https://doi.org/10.1126/science.aar7191

    Article  CAS  Google Scholar 

  42. Somers DJ, Issac P, Edwards K (2004) A high density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor Appl Genet 109:1105–1114

    Article  CAS  PubMed  Google Scholar 

  43. Dolezel J, Macas J, Lucretti S (1999) Flow analysis and sorting of plant chromosomes. Curr Protoc Cytom 9:5.3.1-5.3.33

    Google Scholar 

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Acknowledgements

We thank Dr Ahmed Fawzy Elkot for providing the Egyptian breeding lines/varieties for genotyping. We also gratefully acknowledge Dr Oluwaseyi Shorinola for facilitating the genotyping at John Inns Centre, Norwich, UK.

Funding

This work was carried out under the Sustainable Crop Production Research for International Development (SCPRID). The financial support provided by the Department of Biotechnology, Ministry of Science and Technology, Government of India (grant No. BT/IN/UK/08/PC/2012) and the UK Biotechnology and Biological Sciences Research Council (grants No. BB/JO12017/1 and BB/P016855/1) is gratefully acknowledged. MB, PC and CU gratefully acknowledge the support provided by Monsanto Beachell Borlaug International Scholars Programme (MBBISP).

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Authors and Affiliations

  1. School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141 004, India

    Mitaly Bansal, Puneet Inder Toor, Satinder Kaur & Parveen Chhuneja

  2. John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK

    Nikolai M. Adamski & Cristobal Uauy

  3. Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141 004, India

    Achla Sharma & Puja Srivastava

  4. University of Sydney Plant Breeding Institute-Cobbitty, PMB 4011, Narellan, NSW, 2567, Australia

    Urmil Bansal

Authors
  1. Mitaly Bansal
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  2. Nikolai M. Adamski
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  9. Parveen Chhuneja
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Contributions

MB analysed both genotype and phenotype data and wrote the draft of the manuscript; NMA helped in the assembly of flow sorted chromosome sequence and SNP detection; PIT helped in genotyping the Ae. caudata population; SK maintains the germplasm at PAU, Ludhiana; AS and PS provided the Indian advanced breeding lines and varieties; UB carried out genotyping of the marker on Australian varieties; CU helped in analysis of 5U chromosome data, marker generation and supervised the study; PC conceived the idea, designed and supervised the study, prepared the draft of the manuscript and submitted it. All the authors have read the manuscript and approved it.

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Correspondence to Parveen Chhuneja.

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Supplementary Information

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11033_2021_6525_MOESM1_ESM.xlsx

Supplementary file1 List of commercial varieties/breeding lines from India, Egypt, Australia, and UK along with the score of allele that amplified with XTa5DS-2754099_kasp23 marker (XLSX 19 kb)

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Bansal, M., Adamski, N.M., Toor, P.I. et al. A robust KASP marker for selection of four pairs of linked leaf rust and stripe rust resistance genes introgressed on chromosome arm 5DS from different wheat genomes. Mol Biol Rep 48, 5209–5216 (2021). https://doi.org/10.1007/s11033-021-06525-4

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  • DOI: https://doi.org/10.1007/s11033-021-06525-4

Keywords

  • KASP marker
  • Leaf rust
  • Stripe rust
  • Alien genes
  • Tertiary gene pool
  • Flow sorting